In-House Standard Method for Molecular Characterization of Dissolved Organic Matter by FT-ICR Mass Spectrometry

Spectral and molecular insights into the characteristics of dissolved organic matter in nitrate-contaminated groundwater

The characteristics of dissolved organic matter (DOM) serve as indicators of nitrate pollution in groundwater. However, the specific DOM components associated with nitrate in groundwater systems remain unclear. In this study, dual isotopes of nitrate, three-dimensional Excitation emission matrices (EEMs) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) were utilized to uncover the sources of nitrate and their associations with DOM characteristics. The predominant nitrate in the targeted aquifer was derived from soil organic nitrogen (mean 46.0%) and manure &sewage (mean 34.3%). The DOM in nitrate-contaminated groundwater (nitrate-nitrogen >20 mg/L) exhibited evident exogenous characteristics, with a bioavailable content 2.58 times greater than that of uncontaminated groundwater. Regarding the molecular characteristics, DOM molecules characterized by CHO + 3N, featuring lower molecular weights and H/C ratios, indicated potential for mineralization, while CHONS formulas indicated the exogenous features, providing the potential for accurate traceability. These findings provided insights at the molecular level into the characterization of DOM in nitrate-contaminated groundwater and offer scientific guidance for decision-making regarding the remediation of groundwater nitrate pollution.

The Hunt for Chemical Dark Matter across a River-to-Ocean Continuum

Thousands of mass peaks emerge during molecular characterization of natural dissolved organic matter (DOM) using ultrahigh-resolution mass spectrometry. While mass peaks assigned to certain molecular formulas have been extensively studied, the uncharacterized mass peaks that represent a significant fraction of organic matter and convey biogenic elements and energy have been previously ignored. In this study, we introduce the term dark DOM (DDOM) for unassigned mass peaks and have explored its characteristics and environmental behaviors using a data set of 38 DOM extracts covering the Yangtze River-to-ocean continuum. We identified a total of 9141 DDOM molecules, which exhibited higher molecular weight and greater diversity than the DOM subset with assigned DOM formulas. Although DDOM contributed a smaller fraction of relative abundance, it significantly impacted the molecular weight and molecular composition of bulk DOM. A portion of DDOM with higher molecular weight was found to increase molecular abundance across the river-to-ocean continuum. These compounds could contain halogenated organic molecules and might have a high potential to contribute to the refractory organic carbon pool. With this study, we underline the contribution of dark matter to the total DOM pool and emphasize that more DDOM research is needed to understand its contribution to global biogeochemical cycles and carbon sequestration.

Metagenomic and FT-ICR MS insights into the mechanism for the arsenic biogeochemical cycling in groundwater

Arsenic (As) is a groundwater contaminant of global concern. The degradation of dissolved organic matter (DOM) can provide a reducing environment for As release. However, the interaction of DOM with local microbial communities and how different sources and types of DOM influence the biotransformation of As in aquifers is uncertain. This study used optical spectroscopy, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), metagenomics, and structural equation modeling (SEM) to demonstrate the how the biotransformation of As in aquifers is promoted. The results indicated that the DOM in high-As groundwater is dominated by highly unsaturated low-oxygen(O) compounds that are quite humic and stable. Metagenomics analysis indicated Acinetobacter, Pseudoxanthomonas, and Pseudomonas predominate in high-As environments; these genera all contain As detoxification genes and are members of the same phylum (Proteobacteria). SEM analyses indicated the presence of Proteobacteria is positively related to highly unsaturated low-O compounds in the groundwater and conditions that promote arsenite release. The results illustrate how the biogeochemical transformation of As in groundwater systems is affected by DOM from different sources and with different characteristics.

The loss of dissolved organic matter from biological soil crust at various successional stages under rainfall of different intensities: Insights into the changes of molecular components at different rainfall stages

Biological soil crusts (BSCs) are typical covers in arid and semiarid regions. The dissolved organic matter (DOM) of BSCs can be transported to various aquatic ecosystems by rainfall-runoff processes. However, the spatiotemporal variation in quality and quantity of DOM in runoff remains unclear. Herein, four kinds of runoff plots covered by four successional stages of BSCs were set up on slopes, including bare runoff plot (BR), cyanobacteria crust covered runoff plot (CR), mixed crust covered runoff plot (MIR), and moss crust covered runoff plot (MOR). The quantity and quality of DOM in runoff during rainfall was investigated based on the stimulated rainfall experiments combined with optical spectroscopy and ultra-high resolution mass spectrometry analyses. The results showed that the DOM concentrations (i.e., 0.30 to 45.25 mg L-1) in runoff followed the pattern of MOR>MIR>CR>BR, and they were exponentially decreased with rainfall duration. The DOM loss rate of BR (8.26 to 11.64 %) was significantly greater than those of CR, MIR, and MOR (0.84 to 3.22 %). Highly unsaturated compounds (HUCs), unsaturated aliphatic compounds (UACs), saturated compounds (SCs), and peptide-like compounds (PLCs) were the dominated compounds of the water extractable DOM from the original soils. Thereinto, PLCs and UACs were more easily leached into runoff during rainfall. The relatively intensity of HUCs in runoff generally decreased with rainfall duration, while the relatively intensities of UACs, PLCs, and SCs slightly increased with rainfall duration. These findings suggested that the DOM loss rate was effectively decreased with the successional of BSCs during rainfall; meanwhile, some labile compounds (e.g., PLCs and UACs) were transported into various aquatic ecosystems by rainfall-runoff processes.

Heavy metal induced shifts in microbial community composition and interactions with dissolved organic matter in coastal sediments

Heavy metals can impact the structure and function of coastal sediment. The dissolved organic matter (DOM) pool plays an important role in determining both the heavy metal toxicity and microbial community composition in coastal sediments. However, how heavy metals affect the interactions between microbial communities and DOM remains unclear. Here, we investigated the influence of heavy metals on the microbial community structure (including bacteria and archaea) and DOM composition in surface sediments of Beibu Gulf, China. Our results revealed firstly that chromium, zinc, cadmium, and lead were the heavy metals contributing to pollution in our studied area. Furthermore, the DOM chemical composition was distinctly different in the contaminated area from the uncontaminated area, characterized by a higher average O/C ratio and increased prevalence of carboxyl-rich alicyclic molecules (CRAM) and highly unsaturated compounds (HUC). This indicates that DOM in the contaminated area was more recalcitrant compared to the uncontaminated area. Except for differences in archaeal diversity between the two areas, there were no significant variations observed in the structure of archaea and bacteria, as well as the diversity of bacteria, across the two areas. Nevertheless, our co-occurrence network analysis revealed that the B2M28 and Euryarchaeota, dominating bacterial and archaeal groups in the contaminated area were strongly related to CRAM. The network analysis also unveiled correlations between active bacteria and elevated proportions of nitrogen-containing DOM molecules. In contrast, the archaea-DOM network exhibited strong associations with nitrogen- and sulfur-containing molecules. Collectively, these findings suggest that heavy metals indeed influence the interaction between microbial communities and DOM, potentially affecting the accumulation of recalcitrant compounds in coastal sediments.

High biodegradability of microbially-derived dissolved organic matter facilitates arsenic enrichment in groundwater: Evidence from molecular compositions and structures

Although biodegradation of organic matter is well-known to trigger enrichment of arsenic (As) in groundwater, the effects of DOM sources and biodegradability on As enrichment remain elusive. In this study, groundwater samples were collected from the Hetao basin to identify DOM source and evaluate biodegradability by using spectral and molecular techniques. Results showed that in the alluvial fan, DOM was mainly sourced from terrestrially derived OM, while DOM in the flat plain was more originated from microbially derived OM. Compared to terrestrially derived DOMs, microbially derived DOMs in groundwater, which had relatively higher H/Cwa ratios, NOSC values and more biodegradable molecules, exhibited higher biodegradability. In the flat plain, microbially derived DOMs with higher biodegradability encountered stronger biodegradation, facilitating the reductive dissolution of Fe(III)/Mn oxides and As enrichment in groundwater. Moreover, the enrichment of As depended on the biodegradable molecules that was preferentially utilized for primary biodegradation. Our study highlights that the enrichment of dissolved As in the aquifers was closely associated with microbially derived DOM with high biodegradability and high ability for primary biodegradation.

Noise Filtering Algorithm Using Gaussian Mixture Models for High-Resolution Mass Spectra of Natural Organic Matter

High-resolution mass spectra of natural organic matter (NOM) contain a large number of noise signals. These signals interfere with the correct molecular composition estimation during nontargeted analysis because formula-assignment programs find empirical formulas for such peaks as well. Previously proposed noise filtering methods that utilize the profile of the intensity distribution of mass spectrum peaks rely on a histogram to calculate the intensity threshold value. However, the histogram profile can vary depending on the user settings. In addition, these algorithms are not automated, so they are handled manually. To overcome the mentioned drawbacks, we propose a new algorithm for noise filtering in mass spectra. This filter is based on Gaussian Mixture Models (GMMs), a machine learning method to find the intensity threshold value. The algorithm is completely data-driven and eliminates the need to work with a histogram. It has no customizable parameters and automatically determines the noise level for each individual mass spectrum. The algorithm performance was tested on mass spectra of natural organic matter obtained by averaging a different number of microscans (transients), and the results were compared with other noise filters proposed in the literature. Finally, the effect of this noise filtering approach on the fraction of peaks with assigned formulas was investigated. It was shown that there is always an increase in the identification rate, but the magnitude of the effect changes with the number of microscans averaged. The increase can be as high as 15%.

Hydrological alteration drives chemistry of dissolved organic matter in the largest freshwater lake of China (Poyang Lake)

As the largest reactive organic carbon pool, dissolved organic matter (DOM) plays an important role in various biogeochemical processes in lake ecosystems. Recently, climate change-induced extreme events (e.g., floods and droughts) have significantly modified the hydrological patterns of lakes worldwide, and regulated the quality and quantity of DOM. However, the responses of DOM chemistry to hydrological alteration in lakes remain poorly understood. Here we investigated the influences of hydrological alteration on sources, composition, and characteristics of DOM in Poyang Lake, the largest freshwater lake in China, using a combination of bulk chemical, optical and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) techniques. Results show various sources of DOM (autochthonous, allochthonous, and anthropogenic inputs) and significant variations in DOM chemistry across four hydrological periods (the retreating, dry, rising, and flooding periods) in Poyang Lake. During the retreating, rising, and flooding periods, DOM was characterized by higher aromaticity, humification degree, and recalcitrance, and exhibited pronounced allochthonous signatures. In contrast, DOM contained more S-containing molecules and aliphatic compounds during the dry period, displaying relatively stronger autochthonous features. Terrestrial inputs and the lignin-CHOS formation process are likely the primary underlying mechanisms shaping the differences in DOM chemistry in Poyang Lake. Our research demonstrates the significant impacts of hydrological alteration on DOM dynamics, and provides an improved understanding of DOM biogeochemical cycles and carbon cycling in large aquatic systems under global climate change.

Spatial gradients and molecular transformations of DOM, DON and DOS in human-impacted estuarine sediments

Dissolved organic matter (DOM) constitutes the most active fraction in global carbon pools, with estuarine sediments serving as significant repositories, where DOM is susceptible to dynamic transformations. Anthropogenic nitrogen (N) and sulfur (S) inputs further complicate DOM by creating N-bearing DOM (DON) and S-bearing DOM (DOS). This study delves into the spatial gradients and transformation mechanisms of DOM, DON, and DOS in Pearl River Estuary (PRE) sediments, China, using combined techniques of UV-visible spectroscopy, Excitation-emission matrix (EEM) fluorescence spectroscopy, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), and microbial high-throughput sequencing. Results uncovered a distinct spatial gradient in DOM concentration, aromaticity (SUVA254), hydrophobicity (SUVA260), the content of substituent groups including carboxyl, carbonyl, hydroxyl and ester groups (A253/A203) of chromophoric DOM (CDOM), and the abundances of tyrosine/tryptophan-like protein and humic-like substances in fluorophoric DOM (FDOM). These all decreased from upper to lower PRE, accompanied by a decrease in O3S and O5S components, indicating seaward reduction in the contribution of terrestrial OM, especially anthropogenic inputs. Additionally, sediments exhibited a reduction in molecular diversity (number of formulas) of DOM, DON, and DOS from upper to lower PRE, with molecules tending towards a lower nominal oxidation state of carbon (NOSC) and higher bio-reactivity (MLBL), molecular weight (m/z) and saturation (H/C). While molecular composition of DOM remained similar in PRE sediments, the relative abundance of lignin-like substances decreased, with a concurrent increase in protein-like and lipid-like substances in DON and DOS from upper to lower PRE. Mechanistic analysis identified the joint influence of terrestrial OM, anthropogenic N/S inputs, and microbial processes in shaping the spatial gradients of DOM, DON, and DOS in PRE estuarine sediments. This study contributes valuable insights into the intricate spatial gradients and transformations of DOM, DON, and DOS within human-impacted estuarine sediments.

Arsenic biogeochemical cycling association with basin-scale dynamics of microbial functionality and organic matter molecular composition

Geogenic arsenic (As)-contaminated groundwater is a sustaining global health concern that is tightly constrained by multiple interrelated biogeochemical processes. However, a complete spectrum of the biogeochemical network of high-As groundwater remains to be established, concurrently neglecting systematic zonation of groundwater biogeochemistry on the regional scale. We uncovered the geomicrobial interaction network governing As biogeochemical pathways by merging in-field hydrogeochemical monitoring, metagenomic analyses, and ultrahigh resolution mass spectrometry (FT-ICR MS) characterization of dissolved organic matter. In oxidizing to weakly reducing environments, the nitrate-reduction and sulfate-reduction encoding genes (narGHI, sat) inhibited the dissolution of As-bearing iron minerals, leading to lower As levels in groundwater. In settings from weakly to moderately reducing, high abundances of sulfate-reduction and iron-transport encoding genes boosted iron mineral dissolution and consequent As release. As it evolved to strongly reducing stage, elevated abundance of methane cycle-related genes (fae, fwd, fmd) further enhanced As mobilization in part by triggering the formation of gaseous methylarsenic. During redox cycling of N, S, Fe, C and As in groundwater, As migration to groundwater and immobilization in mineral particles are geochemically constrained by basin-scale dynamics of microbial functionality and DOM molecular composition. The study constructs a theoretical model to summarize new perspectives on the biogeochemical network of As cycling.

Enhanced landfill leachate treatment performance by adsorption-assisted membrane distillation

Membrane fouling and high-strength membrane concentrate production are two limitations of membrane distillation (MD) for landfill leachate treatment. In this study, activated carbon- and biochar-based adsorption processes were integrated into a conventional MD system to overcome these limitations. The organic matter fractionations of the leachate were thoroughly investigated during the treatment. Membrane-reversible and irreversible foulants differed remarkably from the inlet leachate in the non-assisted MD system. Specifically, reversible foulants were characterized by a high abundance of humic-like fluorescent components, high-molecular-weight humic-size constituents, peptides, and unsaturated compounds. In contrast, irreversible foulants were enriched with fulvic-like fluorescent components, low-molecular-weight neutrals, unsaturated compounds, and polyphenols. The adsorption-based pre-treatment effectively removed foulant precursors from landfill leachate, with a relatively higher (20%) adsorption performance for specific biochar used in this study than for activated carbon. Compared with the non-assisted MD system, the biochar-assisted MD system showed improved performance, achieving 40% overall membrane flux recovery, 42% higher filtration fluxes, and 53% lower concentrate production. In addition, a 15% higher removal of irreversible foulants was observed as compared to the reversible foulants, which can potentially increase the membrane lifespan. This study demonstrates the effectiveness of an adsorption-assisted MD system supported by increased filtration, membrane fouling alleviation, and low-strength leachate concentrate generation.

Evolution of dissolved organic nitrogen chemistry during transportation to the marginal sea: Insights from nitrogen isotope and molecular composition analyses

Estuaries are hotspots where terrestrially originated dissolved organic matter (DOM) is modified in molecular composition before entering marine environments. However, very few research has considered nitrogen (N) modifications of DOM molecules in estuaries, limiting our understanding of dissolved organic nitrogen (DON) cycling and the associated carbon cycling in estuaries. This study integrated optical, stable isotopes (δ15N and δ13C) and molecular composition (FT-ICR MS) to characterize the transformation of DOM in the Yangtze River Estuary. Both concentration of dissolved organic carbon (DOC) and DON decreased with increasing salinity, while their δ13C and δ15N increased with the increasing salinity. A significant positive correlation was found between δ15N and δ13C during the transportation of DOM to marginal seas, indicating that the behavior of both DOC and DON are primarily controlled by the mixing of freshwater and the seawater in the YRE. During the mixing process, the DON addition was observed using the conservative mixing curves. In the view of molecular composition, DOM molecules became more aromatic as the number of N atoms increased. Spearman correlations reveal that DOM molecules with fewer N atoms exhibited a higher enrichment in protein-like components, while those with more N atoms were more enriched in humic-like components. In addition, the δ15N and δ13C tended to increase as the N content of DOM decreased. Therefore, DON molecules with fewer N atoms were likely to be transformed into those with more N atoms based on the isotopic fractionation theory. This study establishes a linkage between the molecular composition and the δ15N of DOM, and discovers the N transformation pattern within DOM molecules during the transportation to marginal seas.

Molecular formula assignment of dissolved organic matter by ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry using two non-targeted data processing approaches: A case study from recirculating aquaculture systems

BACKGROUND

The accumulation of dissolved organic matter (DOM) poses an issue in the management of the water quality from recirculating aquaculture systems (RAS), but its characterization is often not detailed enough to understand the DOM transformations in RAS. In this study, we investigated the application of two distinct non-targeted data processing approaches using ultra-performance liquid chromatography (UPLC) with quadrupole time-of-flight mass spectrometry (QTOF-MS) and two software with different algorithmic designs: PetroOrg and Progenesis QI to accurately characterize the molecular composition of DOM in RAS by UPLC-QTOF-MS.

RESULTS

The UPLC-QTOF-MS resolution in combination with PetroOrg and Progenesis QI software successfully assigned 912 and 106 unique elemental compositions, respectively, including compounds containing carbon, hydrogen, and oxygen (CHO) and nitrogen-containing CHO compounds (CHON), in the DOM samples from RAS. The results of these two distinct data processing approaches were consistent with the list of DOM formulas from RAS identified by higher resolution mass spectrometry techniques confirming their reliability. PetroOrg approach revealed only compositional information in the DOM samples from RAS, while Progenesis QI in addition to identifying new elemental compositions, increased their chemical space by giving information about their polarity and their possible key structures. DOM samples from RAS were found to be rich in unsaturated CHO compounds, with tentatively key structures of terpenoids with medium polarity indicating natural origins in their composition. The analysis also revealed probable structures of sucrose fatty acid esters and polyethylene glycol, indicating anthropogenic sources.

SIGNIFICANCE AND NOVELTY

The combination of these two non-targeted data processing approaches significantly improves the characterization of the complex mixture of DOM from RAS by UPLC-QTOF-MS reporting for the first time accurate DOM results in terms of its composition, while proposing its key structures. The presented methods can also be used to analyze different DOM samples with other HRMS techniques and software.

Solid-Phase Extraction at High pH as a Promising Tool for Targeted Isolation of Biologically Active Fractions of Humic Acids

A search for novel sources of biologically active compounds is at the top of the agenda for biomedical technologies. Natural humic substances (HSs) contain a large variety of different chemotypes, such as condensed tannins, hydrolyzable tannins, terpenoids, lignins, etc. The goal of this work was to develop an efficient separation technique based on solid-phase extraction (SPE) for the isolation of narrow fractions of HS with higher biological activity compared to the initial material. We used lignite humic acid as the parent humic material, which showed moderate inhibition activity toward beta-lactamase TEM 1 and antioxidant activity. We applied two different SPE techniques: the first one was based on a gradient elution with water/methanol mixtures of the humic material sorbed at pH 2, and the second one implied separation by a difference in the pKa value by the use of sequential sorption of HS at pH from 8 to 3. SPE cartridges Bond Elute PPL (Agilent) were used in the fractionation experiments. The first and second techniques yielded 9 and 7 fractions, respectively. All fractions were characterized using high-resolution mass spectrometry and biological assays, including the determination of beta-lactamase (TEM 1) inhibition activity and antioxidant activity. The acidity-based separation technique demonstrated substantial advantages: it enabled the isolation of components, outcompeting the initial material at the first step of separation (sorption at pH 8). It showed moderate orthogonality in separation with regard to the polarity-based technique. Good perspectives are shown for developing a 2D separation scheme using a combination of polarity and acidity-based approaches to reduce structural heterogeneity of the narrow fractions of HS.

Dispersant-enhanced photodissolution of macondo crude oil: A molecular perspective

Previous laboratory studies developed a conceptual model based on elevated non-volatile dissolved organic carbon (NVDOC) concentrations after photodegradation and subsequent dissolution of Macondo oil following the Deepwater Horizon blowout. However, those experiments did not account for the effects of ∼1 million gallons of dispersant applied to the surface oil. Here, laboratory results show photodissolution in the presence of dispersant results in > 2x increase in NVDOC concentrations after extensive photoprocessing relative to oil without dispersant. This result corresponds with an apparent increase in the percentage of surface oil photodissolution from approximately 4% in the absence of dispersant to 7% in the presence of dispersant. The oil and dissolved products were analyzed by excitation-emission matrix spectroscopy and ultrahigh resolution mass spectrometry. The compounds that persisted in the oil phase are relatively aromatic without dispersant, while those in the presence of dispersant are highly aliphatic, paraffinic, wax-like compounds. The composition of the dissolved compounds produced from both treatment types are nearly identical after 240 h of exposure to simulated sunlight. The NVDOC and chemical composition information indicate that the photodissolution of MC252 oil in the presence of dispersant is enhanced and accelerated, suggesting that the effects of dispersants should be included in mass transfer calculations from the oil to the aqueous phase.

Hypoxia diversifies molecular composition of dissolved organic matter and enhances preservation of terrestrial organic carbon in the Yangtze River Estuary

Dissolved organic matter (DOM) is an essential component of the global carbon cycle, and estuaries link the rivers and the oceans, thus playing important roles in land-ocean DOM transformation and transport. However, the effects of hypoxia on DOM transport and fate in estuaries and coastal oceans remains poorly understood. To address this gap, we characterized the molecular composition of DOM in bottom water (BW) and sediment porewater (PW) at hypoxic and non-hypoxic sites in the Yangtze River Estuary (YRE) using ultra-high-resolution Fourier transform ion cyclotron resonance mass spectrometry. Our results showed significant differences in DOM molecular composition between hypoxic and non-hypoxic areas for both BW and PW. Specifically, DOM in hypoxic sites was more recalcitrant than that in non-hypoxic areas for both BW and PW, with lower H/C, and higher O/C, double bond equivalent, and modified aromaticity index. The presence of higher polyphenols, and black carbon in hypoxic areas suggested that hypoxic conditions could facilitate the preservation of terrestrial organic matter. Furthermore, we identified a much higher number of hypoxia-unique formulas than ocean-non-hypoxia-unique formulas, indicating that hypoxia could diversify the DOM pool. Within hypoxia-unique formulas for PW, both biologically labile (unsaturated aliphatic compounds and peptides) and recalcitrant formulas (carboxyl-rich alicyclic molecules) were found, suggesting that hypoxia could facilitate the preservation of labile formulas and the production of recalcitrant formulas. In addition, we formulated that the sulfurization is more important in PW than BW in hypoxic areas based on the higher dissolved organic sulfur (DOS) abundance and larger number of hypoxia-only formulas in hypoxic PW, and also the precursor analysis results. Overall, our study provides insights into the effect of hypoxia on the molecular characteristics and preservation of DOM in estuaries and coastal oceans, highlighting the importance of considering hypoxia in understanding the biogeochemical processes of these ecosystems.

Effect of salinity on molecular characterization of dissolved organic matter using ESI FT-ICR MS

Solid-phase extraction (SPE) coupled with negative-ion Electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) has been widely used for molecular characterization of dissolved organic matter (DOM). However, little attention has paid to test whether the salinity of the sample and the presence of chloride ions in water samples affect the molecular composition of DOM extracted by SPE (SPE-DOM). In this study, one natural organic matter standard and several natural waters were selected to investigate how salinity affects the molecular composition of SPE-DOM and the selectivity of chloride ion adducts formation with respect to the molecular structure of SPE-DOM in negative ion ESI FT-ICR MS analysis. The results show that the molecular composition of SPE-DOM varied in a sample made by different salinity; and the variation pattern of DOM composition was different among different water samples under the treatment of consistent salinity gradients. The chloride ions can't be completely removed from cartridges in conventional SPE, thus leading organic compounds in SPE-DOM to form [M+Cl]‾ adducts when performing ESI FT-ICR MS analysis. In addition, the molecules with high H/C and low O/C ratios were likely to form [M+Cl]‾ ions. The relative abundance of [M+Cl]‾ ions could increase with the increase of salinity. These results are instructive to guide the pretreatment and molecular characterization of DOM in water samples with different salinity. Overall, we proposed a modification to the SPE to minimum reduce the formation of chloride ion adducts during the isolation of DOM.

Mitigation of soil N2O emissions by decomposed straw based on changes in dissolved organic matter and denitrifying bacteria

The return of decomposed straw represents a less explored potential option for reducing N2O emissions. However, the mechanisms underlying the effects of decomposed straw return on soil N2O mitigation are still not fully clear. Therefore, we used a helium atmosphere robotized continuous flow incubation system to compare the soil N2O and N2 emissions from four treatments: CK (control: no straw), WS (wheat straw), IWS (wheat straw decomposed with Irpex lacteus), and PWS (wheat straw decomposed with Phanerochaete chrysosporium). All the treatments have been fertilized with the same amount of KNO3. Furthermore, we also analyzed i) the chemodiversity of soil dissolved organic matter (DOM), ii) the nirS, nirK, and nosZ gene copies and relative abundances of denitrifying bacterial communities (DBCs), and iii) the specific linkages between N2O emissions and DOM and DBC. The results showed that the WS, IWS and PWS treatments increased N2O emissions compared to the CK treatment. However, applying decomposed straw to soil, especially straw treated with P. chrysosporium, effectively decreased the soil N2O and increased N2 emissions compared to WS and IWS. Moreover, the IWS and PWS treatments increased the CHO composition, but they decreased the CHON and CHOS compositions of heteroatomic compounds of DOM compared with the WS and CK treatments. Furthermore, the WS, IWS and PWS treatments all significantly increased the nirS and nosZ gene copies compared with the CK treatment. Additionally, compared with the other treatments, the PWS treatment significantly shaped the DBC and led to a higher relative abundance of Pseudomonas with nirS and nosZ genes. Meanwhile, Network analysis showed that the mitigation of N2O was closely related to particular DOM molecules, and specific DBC taxa. These results highlight the potential for decomposed straw amendments to mitigate of soil N2O emissions not only by changing soil DOM but also mediating the soil DBC.

Molecular comparison of organic matter removal from shale gas flowback wastewater: Ozonation versus Fenton process

Shale gas extraction process generates a large amount of shale gas flowback wastewater (SGFW) containing refractory organic compounds, which can pose serious environmental threats if not properly treated. However, the extremely complex compositions of organics in SGFW are still unknown and their transformation pathways in O3- and •OH-dominated systems are not well recognized, which restrain the selection of treatment technology and optimization of operational parameters. The removal characteristics and reaction mechanism of dissolved organic matter (DOM) in SGFW treated by ozonation and Fenton processes were comparatively investigated using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. The results showed that both processes could degrade low-oxygen highly unsaturated and phenolic organics, polyphenolics and polycyclic aromatics, and transform them into aliphatic organics and high-oxygen highly unsaturated and phenolic organics. With increasing action of reactive oxygen species (O3 for ozonation and •OH for Fenton process), the degradation products (mainly aliphatic organics) increased during ozonation. However, in Fenton process, a wider range of DOM was removed without aliphatic organics accumulation. The degradation mechanisms of DOM during ozonation and Fenton processes included oxygen addition reactions (+3O, +H2O2, and +2O) as dominant pathways. However, ozonation showed more violent oxygenation, hydroxylation, and carboxylation, while Fenton process presented more violent chain-breaking reactions. These results revealed the selective oxidation of ozone and nonselective oxidation of •OH during SGFW treatment, and provided theoretical support for selecting SGFW treatment approaches.

Molecular Characteristics and Formation Mechanisms of Unknown Ozonation Byproducts during the Treatment of Flocculated Nanofiltration Leachate Concentrates Using O3 and UV/O3 Processes

Both ozone (O3) and UV/O3 treatment processes can effectively remove organic matter in the flocculated membrane filtration concentrate from landfill leachate, but the ozonation byproducts (OBPs) generated in the processes remain unknown. Using electrospray ionization-coupled Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS), this study investigated the molecular characteristics of unknown OBPs and their formation mechanisms during the treatment of flocculated nanofiltration concentrate (FNFC) using the O3 and UV/O3 processes. The results showed that after being treated by the O3 and UV/O3 processes, the average value of the oxygen-to-carbon ratio (O/Cavg) in the FNFC organic matter increased substantially from 0.49 to 0.61-0.64 and 0.63-0.71, respectively, with an O3 dosage of 13.4-54.4 mg/min. The main OBPs were CHO and CHON compounds, which were mainly produced through oxygenation (+O2/+O3 and -H2+O2), oxidative deamination (-NH3+O2), decyclopropyl (-C3H4), and deisopropyl (-C3H6) reactions. The hydroxyl radical (•OH) can intensify these reactions, resulting in an abundance of OBPs with a high oxidation degree and low molecular weight. OBPs at five m/z values were fragmented and analyzed with tandem mass spectrometry, and abundant hydroxyl groups, carboxyl groups, and carbonyl groups were tentatively identified, presenting a potential toxicity to aquatic organisms. Due to the high molecular diversity of the OBPs in FNFC, their lower ΔGCoxo compared to natural fulvic acid, and potential toxicity, their impact on the water environment should be given more attention.

Unraveling the Linkages between Molecular Abundance and Stable Carbon Isotope Ratio in Dissolved Organic Matter Using Machine Learning

Dissolved organic matter (DOM) is a complex mixture of molecules that constitutes one of the largest reservoirs of organic matter on Earth. While stable carbon isotope values (δ13C) provide valuable insights into DOM transformations from land to ocean, it remains unclear how individual molecules respond to changes in DOM properties such as δ13C. To address this, we employed Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to characterize the molecular composition of DOM in 510 samples from the China Coastal Environments, with 320 samples having δ13C measurements. Utilizing a machine learning model based on 5199 molecular formulas, we predicted δ13C values with a mean absolute error (MAE) of 0.30‰ on the training data set, surpassing traditional linear regression methods (MAE 0.85‰). Our findings suggest that degradation processes, microbial activities, and primary production regulate DOM from rivers to the ocean continuum. Additionally, the machine learning model accurately predicted δ13C values in samples without known δ13C values and in other published data sets, reflecting the δ13C trend along the land to ocean continuum. This study demonstrates the potential of machine learning to capture the complex relationships between DOM composition and bulk parameters, particularly with larger learning data sets and increasing molecular research in the future.

Temperature Thresholds of Pyrogenic Dissolved Organic Matter in Heating Experiments Simulating Forest Fires

Heating temperature (HT) during forest fires is a critical factor in regulating the quantity and quality of pyrogenic dissolved organic matter (DOM). However, the temperature thresholds at which maximum amounts of DOM are produced (TTmax) and at which the DOC gain turns into net DOC loss (TT0) remain unidentified on a component-specific basis. Here, based on solid-state 13C nuclear magnetic resonance, absorbance and fluorescence spectroscopies, and Fourier transform ion cyclotron resonance mass spectrometry, we analyzed variations in DOM composition in detritus and soil with HT (150-500 °C) and identified temperature thresholds for components on structural, fluorophoric, and molecular formula levels. TTmax was similar for detritus and soil and ranged between 225 and 250 °C for bulk dissolved organic carbon (DOC) and most DOM components. TT0 was consistently lower in detritus than in soil. Moreover, temperature thresholds differed across the DOM components. As the HT increased, net loss was observed initially in molecular formulas tentatively associated with carbohydrates and aliphatics, then proteins, peptides, and polyphenolics, and ultimately condensed aromatics. Notably, at temperatures lower than TT0, particularly at TTmax, burning increased the DOC quantity and thus might increase labile substrates to fuel soil microbial community. These composition-specific variations of DOM with temperature imply nonlinear and multiple temperature-dependent wildfire impacts on soil organic matter properties.

Enhanced sequestration of uranium by coexisted lead and organic matter during ferrihydrite transformation

The dynamic reactions of uranium (U) with iron (Fe) minerals change its behaviors in soil environment, however, how the coexisted constituents in soil affect U sequestration and release on Fe minerals during the transformation remains unclear. Herein, coupled effects of lead (Pb) and dissolved organic matter (DOM) on U speciation and release kinetics during the catalytic transformations of ferrihydrite (Fh) by Fe(II) were investigated. Our results revealed that the coexistence of Pb and DOM significantly reduced U release and increased the immobilization of U during Fh transformation, which were attributed to the enhanced inhibition of Fh transformation, the declined release of DOM and the increased U(VI) reduction. Specifically, the presence of Pb increased the coprecipitation of condensed aromatics, polyphenols and phenols, and these molecules were preferentially maintained by Fe (oxyhydr)oxides. The sequestrated polyphenols and phenols could further facilitate U(VI) reduction to U(IV). Additionally, a higher Pb content in coprecipitates caused a slower U release, especially when DOM was present. Compared with Pb, the concentrations of the released U were significantly lower during the transformation. Our results contribute to predicting U sequestration and remediating U-contaminated soils.

Quantifying Stochastic Processes in Shaping Dissolved Organic Matter Pool with High-Resolution Mass Spectrometry

Natural dissolved organic matter (DOM) represents a ubiquitous molecular mixture, progressively characterized by spatiotemporal resolution. However, an inadequate comprehension of DOM molecular dynamics, especially the stochastic processes involved, hinders carbon cycling predictions. This study employs ecological principles to introduce a neutral theory to elucidate the fundamental processes involving molecular generation, degradation, and migration. A neutral model is thus formulated to assess the probability distribution of DOM molecules, whose frequencies and abundances follow a β-distribution relationship. The neutral model is subsequently validated with high-resolution mass spectrometry (HRMS) data from various waterbodies, including lakes, rivers, and seas. The model fitting highlights the prevalence of molecular neutral distribution and quantifies the stochasticity within DOM molecular dynamics. Furthermore, the model identifies deviations of HRMS observations from neutral expectations in photochemical and microbial experiments, revealing nonrandom molecular transformations. The ecological null model further validates the neutral modeling results, demonstrating that photodegradation reduces molecular stochastic dynamics at the surface of an acidic pit lake, while random distribution intensifies at the river surface compared with the porewater. Taken together, the DOM molecular neutral model emphasizes the significance of stochastic processes in shaping a natural DOM pool, offering a potential theoretical framework for DOM molecular dynamics in aquatic and other ecosystems.

Molecular composition of dissolved organic matter across diverse ecosystems: Preliminary implications for biogeochemical cycling

Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) has been widely applied to characterize the molecular composition of dissolved organic matter (DOM) in different ecosystems. Most previous studies have explored the molecular composition of DOM focused on one or a few ecosystems, which prevents us from tracing the molecular composition of DOM from different sources and further exploring its biogeochemical cycling across ecosystems. In this study, a total of 67 DOM samples, including soil, lake, river, ocean, and groundwater, were analyzed by negative-ion electrospray ionization FT-ICR MS. Results show that molecular composition of DOM varies dramatically among diverse ecosystems. Specifically, the forest soil DOM exhibited the strongest terrestrial signature of molecules, while the seawater DOM showed the most abundant of biologically recalcitrant components, for example, the carboxyl-rich alicyclic molecules were abundant in the deep-sea waters. Terrigenous organic matter is gradually degraded during its transport along the river-estuary-ocean continuum. The saline lake DOM showed similar DOM characteristics with marine DOM, and sequestrated abundant recalcitrant DOM. By comparing these DOM extracts, we found that human activities likely lead to an increase in the content of S and N-containing heteroatoms in DOM, this phenomenon was commonly found in the paddy soil, polluted river, eutrophic lake, and acid mine drainage DOM samples. Overall, this study compared molecular composition of DOM extracted from various ecosystems, providing a preliminary comparison on the DOM fingerprint and an angle of view into biogeochemical cycling across different ecosystems. We thus advocate for the development of a comprehensive molecular fingerprint database of DOM using FT-ICR MS across a wider range of ecosystems. This will enable us to better understand the generalizability of the distinct features among ecosystems.

Photo-transformation of wastewater effluent organic matter reduces the formation potential and toxicity of chlorinated disinfection byproducts

Sunlight exposure can degrade and transform discharged wastewater effluent organic matter (EfOM) in aquatic systems, potentially enhancing the feasibility of reusing wastewater for drinking purposes. However, there remains a lack of comprehensive understanding regarding the sunlight-induced changes in the molecular-level composition, characteristics, and chlorine reactivity of EfOM. Herein, we investigated the impact of sunlight on the optical properties, chemical composition, and formation of disinfection byproducts of EfOM using multiple spectroscopic analyses, high-resolution mass spectrometry, chlorination experiments, and in vitro bioassays. Upon natural sunlight exposure, we observed significant decreases in ultraviolet-visible absorbance and fluorescence intensity of EfOM, indicating the destruction of chromophores and fluorophores. Photolysis generally yields products with lower molecular weight and aromaticity, and with higher saturation and oxidation levels. Moreover, a shift within the EfOM from condensed aromatic-like compounds to tannin-like components was observed. Furthermore, sunlight exposure reduced the reactivity of EfOM toward the formation of trihalomethanes and haloacetonitriles during chlorination, while there was a slight increase in the specific formation potential of haloketones. Importantly, the disinfection byproducts resulting from chlorination of the irradiated EfOM exhibited reduced microtoxicity. Overall, this study provides new insights into alterations in EfOM under sunlight exposure and aids in predicting the health risks of effluent discharge in water environments.

Spatial and molecular variations in forest topsoil dissolved organic matter as revealed by FT-ICR mass spectrometry

Forest soils cover about 30 % of the Earth's land surface and play a fundamental role in the global cycle of organic matter. Dissolved organic matter (DOM), the largest active pool of terrestrial carbon, is essential for soil development, microbial metabolism and nutrient cycling. However, forest soil DOM is a highly complex mixture of tens of thousands of individual compounds, which is largely composed of organic matter from primary producers, residues from microbial process and the corresponding chemical reactions. Therefore, we need a detailed picture of molecular composition in forest soil, especially the pattern of large-scale spatial distribution, which can help us understand the role of DOM in the carbon cycle. To explore the spatial and molecular variations of DOM in forest soil, we choose six major forest reserves located in different latitudes ranging in China, which were investigated by Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS). Results show that aromatic-like molecules are preferentially enriched in DOM at high latitude forest soils, while aliphatic/peptide-like, carbohydrate-like, and unsaturated hydrocarbon molecules are preferentially enriched in DOM at low latitude forest soils, besides, lignin-like compounds account for the highest proportion in all forest soil DOM. High latitude forest soils have higher aromatic equivalents and aromatic indices than low latitude forest soils, which suggest that organic matter at higher latitude forest soils preferentially contain plant-derived ingredients and are refractory to degradation while microbially derived carbon is dominant in organic matter at low latitudes. Besides, we found that CHO and CHON compounds make up the majority in all forest soil samples. Finally, we visualized the complexity and diversity of soil organic matter molecules through network analysis. Our study provides a molecular-level understanding of forest soil organic matter at large scales, which may contribute to the conservation and utilization of forest resources.

Transformation of dissolved organic matter and related arsenic mobility at a surface water-groundwater interface in the Hetao Basin, China

Porewater arsenic mobility above the groundwater table has been recognized as a potential cause of arsenic-rich groundwater, but the processing pathways of dissolved organic matter (DOM) in that hyporheic zone and their effect on porewater arsenic release remain poorly understood. To address these issues, two porewater profiles were sampled in a surface water-groundwater interaction zone from the Hetao Basin, China, to monitor the porewater geochemistry and DOM molecular characteristics. The results show that the porewater arsenic, Fe(II), and DOC concentrations were all significantly higher than those of the intruding pond water, and were located above the conservative mixing model lines. This indicates a net release of these solutes from the sediment. By comparing the porewater with pond water DOM, we found that the carboxyl-rich alicyclic molecules (CRAM) were selectively preserved, carbohydrates and aliphatics/proteins were preferentially consumed, and low O/C-ratio compounds with high bioproduction index (I_bioprod) and terrestrial index (I_terr) were produced. The transformation of CHO to CHOS compounds also represented a pathway of recalcitrant DOM production. The produced recalcitrant organic compounds mostly contributed to the elevated porewater DOC concentrations, but their contribution decreased along the filtration path. The consumption of labile DOM compounds would be responsible for Fe(III) hydroxide reduction and arsenic release. The generated recalcitrant DOM may also be a driver of porewater arsenic mobility by acting as electron shuttles. This study highlights the importance of the hyporheic zone in shaping shallow groundwater DOM composition and the potential contribution to arsenic enrichment.

Molecular insight into the transformation of dissolved organic matter during sewage sludge composting: An investigation of a full-scale composting plant

The aim of the study was to explore the molecular dynamics and transformation pathways of dissolved organic matter (DOM) in sewage sludge (SS) during composting, and the DOM of raw material, material experiencing thermophilic phase and material collected from humification phase were characterized using electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry. The results indicated that there were approximately 85% of aliphatic/proteins and 75% of carbohydrate preferentially decomposed in the thermophilic phase. Moreover, lignins/carboxylic-rich alicyclic molecules (CRAM) were the main N-containing substances evolved in the decomposition, which leading to a reduction of N/C ratio from 0.073 to 0.041. Whereas aliphatic acids and tryptophan in lignins/CRAM with high oxidizing capacities are preferentially decomposed in the thermophilic phase. As for maturity phase, the carbon of the newly generated compounds (belonging to lignins/CRAM and tannins), possessed an oxidation state that similar to sulfonates and sulfonamides, and these DOM are beneficial for the humic substances formation. Moreover, it was found that the newly formed N2Ox and N3Ox compounds had a more significant contribution to the double bond equivalent (DBE) of the compost, corresponding to 1.0 and 1.7 DBE, respectively. The results would help explore the understanding of DOM transformation and humification during SS composting in the microscopic molecular level.

Molecular-level insights into the heterogeneous variations and dynamic formation mechanism of leached dissolved organic matter during the photoaging of polystyrene microplastics

Microplastics (MPs) and their derivatives have received worldwide attention owing to their adverse effects on ecosystems. However, molecular diversity and dynamic formation of dissolved organic matter (DOM) during the photoaging of MPs remain unclear. Herein, we explored a molecular‒level formation mechanism for polystyrene MP (MPPS)‒derived DOM (PSDOM) during the photoaging of MPs to explain the evolution, heterogeneity, and sequential response of molecules to irradiation. Two‒dimensional correlation spectroscopy was applied to correlate the variations of PSDOM molecules detected by Fourier transform-ion cyclotron resonance mass spectrometry with those of MPPS functional groups detected by Fourier transform infrared spectroscopy. Irradiation‒induced PSDOM contained the most highly unsaturated structures with oxygen, but showed fewer aromatic structures than natural aquatic DOM. Photochemical transformations occurred between saturated‒reduced and oxidized molecules during PSDOM leaching, with the low‒oxidized and high‒oxidized molecules undergoing considerable changes in the normal carbon oxidation state and molecular number, respectively. The primary sequential response of PSDOM molecules to increasing irradiation time [low‒oxidized/high‒weight (450 Collapse

Key Words

• Dynamic formation
• Fluorescence properties
• Heterogeneous correlations
• Leaching responses
• Molecular parameters
• Unique molecules

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MESH Headings

• Microplastics
• Polystyrenes
• Plastics
• Dissolved Organic Matter
• Ecosystem
• Skin Aging

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Grants Collapse

Affiliation(s)

Fanhao Song State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
Tingting Li State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; School of Environment, Tsinghua University, Beijing 100084, China
Jin Hur Department of Environment and Energy, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, South Korea
Quan Shi State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China
Fengchang Wu State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
Wei He Ministry of Education Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
Di Shi State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
Chen He State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China
Lingfeng Zhou State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
Mingqi Ruan State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
Yuhan Cao State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China

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Niche differentiation of microbial community shapes vertical distribution of recalcitrant dissolved organic matter in deep-sea sediments

Sedimentary organic matter provides carbon substrates and energy sources for microorganisms, which drive benthic biogeochemical processes and in turn modify the quantity and quality of dissolved organic matter (DOM). However, the molecular composition and distribution of DOM and its interactions with microbes in deep-sea sediments remain poorly understood. Here, molecular composition of DOM and its relationship with microbes were analyzed in samples collected from two sediment cores (∼40 cm below the sea floor), at depths of 1157 and 2253 m from the South China Sea. Results show that niche differentiation was observed on a fine scale in different sediment layers, with Proteobacteria and Nitrososphaeria dominating the shallow sediments (0-6 cm) and Chloroflexi and Bathyarchaeia prevailing in deeper sediments (6-40 cm), indicating correspondence of microbial community composition with both geographical isolation and the availability of organic matter. An intimate link between the DOM composition and microbial community further indicates that, microbial mineralization of fresh organic matter in the shallow layer potentially resulted in the accumulation of recalcitrant DOM (RDOM), while relatively low abundance of RDOM was linked to anaerobic microbial utilization in deeper sediment layers. In addition, higher RDOM abundance in the overlying water, as compared to that in the surface sediment, suggests that sediment might be a source of deep-sea RDOM. These results emphasize the close relation between the distribution of sediment DOM and different microbial community, laying a foundation for understanding the complex dynamics of RDOM in deep-sea sediment and water column.

Implications of the Cultivation of Rosemary and Thyme (Lamiaceae) in Plant Communities for the Development of Antioxidant Therapies

Oxidative stress is the most critical factor in multiple functional disorders' development, and natural antioxidants could protect the human body against it. Our study aims to investigate the polyphenol content of four extracts of two medicinal plants (Rosmarinus officinalis L. and Thymus vulgaris L.) and analyze the correlation with their antioxidant activity. The research was carried out on extracts of rosemary and thyme obtained from species cultivated together in plant communities. Both were compared with extracts from species cultivated in individual crops (control crops). Their polyphenols were determined by spectrophotometric methods (dosage of flavones, phenol carboxylic acids, and total polyphenols) and chromatography (UHPLC-MS and FT-ICR MS). Triterpenic acids were also quantified, having a higher concentration in the thyme extract from the culture. The antioxidant activity of the dry extracts was evaluated in vitro (DPPH, ABTS, and FRAP) and in silico (prediction of interactions with BACH1/BACH2 transcription factors). The concentrations of polyphenols are higher in the extracts obtained from the sources collected from the common crops. These observations were also validated following the chromatographic analysis for some compounds. Statistically significant differences in the increase in the antioxidant effect were observed for the extracts from the common batches compared to those from the individual ones. Following the Pearson analysis, the IC₅₀ values for each plant extract were strongly correlated with the concentration of active phytoconstituents. Molecular docking studies revealed that quercetin could bind to BTB domains of BACH1 and BACH2 transcription factors, likely translating into increased antioxidant enzyme expression. Future studies must validate the in silico findings and further investigate phytosociological cultivation's effects.

Integrated FT-ICR MS and metabolome reveals diatom-derived organic matter by bacterial transformation under warming and acidification

Bacterial transformation and processing of diatom-derived organic matter (OM) is extremely important for the cycling of production and energy in marine ecosystems; this process contributes to the production of microbial food webs. In this study, a cultivable bacterium (Roseobacter sp. SD-R1) from the marine diatom Skeletonema dohrnii were isolated and identified. A combined Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS)/untargeted metabolomics approach was used to synthesize the results of bacterial transformation with dissolved OM (DOM) and lysate OM (LOM) under warming and acidification through laboratory experiments. Roseobacter sp. SD-R1 had different preferences for the conversion of molecules in S. dohrnii-derived DOM and LOM treatments. The effects of warming and acidification contribute to the increased number and complexity of molecules of carbon, hydrogen, oxygen, nitrogen, and sulfur after the bacterial transformation of OM. The chemical complexity generated by bacterial metabolism provides new insights into the mechanisms that shape OM complexity.

Temperature-Dependent Molecular Evolution of Biochar-Derived Dissolved Black Carbon and Its Interaction Mechanism with Polyvinyl Chloride Microplastics

Biochar-derived dissolved black carbon (DBC) molecules are dependent on the BC formation temperature and affect the fate of emerging contaminants in waters, such as polyvinyl chloride microplastic (MP_PVC). However, the temperature-dependent evolution and MP_PVC-interaction of DBC molecules remain unclear. Herein, we propose a novel DBC-MP_PVC interaction mechanism by systematically interpreting heterogeneous correlations, sequential responses, and synergistic relationships of thousands of molecules and their linking functional groups. Two-dimensional correlation spectroscopy was proposed to combine Fourier transform-ion cyclotron resonance mass spectrometry and spectroscopic datasets. Increased temperature caused diverse DBC molecules and fluorophores, accompanied by molecular transformation from saturation/reduction to unsaturation/oxidation with high carbon oxidation states, especially for molecules with acidic functional groups. The temperature response of DBC molecules detected via negative-/positive-ion electrospray ionization sequentially occurred in unsaturated hydrocarbons → lignin-like → condensed aromatic → lipid-/aliphatic-/peptide-like → tannin-like → carbohydrate-like molecules. DBC molecular changes induced by temperature and MP_PVC interaction were closely coordinated, with lignin-like molecules contributing the most to the interaction. Functional groups in DBC molecules with m/z < 500 showed a sequential MP_PVC-interaction response of phenol/aromatic ether C-O, alkene C═C/amide C═O → polysaccharides C-O → alcohol/ether/carbohydrate C-O groups. These findings help to elucidate the critical role of DBCs in MP environmental behaviors.

Molecular signatures of soil-derived dissolved organic matter constrained by mineral weathering

Dissolved organic matter (DOM) in soils drives biogeochemical cycling and soil functions in different directions depending on its molecular signature. Notably, there is a distinct paucity of information concerning how the molecular signatures of soil DOM vary with different degrees of weathering across wide geographic scales. Herein, we resolved the DOM molecular signatures from 22 diverse Chinese reference soils and linked them with soil organic matter and weathering-related mineralogical properties. The mixed-effects models revealed that the yields of DOM were determined by soil organic carbon content, whereas the molecular signature of DOM was primarily constrained by the weathering-related dimension. The soil weathering index showed a positive effect on the lability and a negative effect on the aromaticity of DOM. Specifically, DOM in highly weathered acidic soils featured more amino sugars, carbohydrates, and aliphatics, as well as less O-rich polyphenols and condensed aromatics, thereby conferring a higher DOM biolability and lower DOM aromaticity. This study highlights the dominance of the weathering-related dimension in constraining the molecular signatures and potential functions of DOM in soils across a wide geographic scale.

Dissolved organic matter composition and fluorescence characteristics of the river affected by coal mine drainage

Coal mine drainage (CMD) discharged into surface waters results in serious environmental pollution risk to rivers, lakes, and reservoirs. Coal mine drainage generally contains a variety of organic matter and heavy metals due to coal mining activities. Dissolved organic matter (DOM) plays an important role in the physicochemical and biological processes of many aquatic ecosystems. In this study, the investigations were carried out in the dry and wet seasons in 2021 to assess the characteristics of DOM compounds in coal mine drainage and the CMD-affected river. The results indicated that the pH of CMD-affected river pressed close to coal mine drainage. Besides, coal mine drainage lowered DO by 36% and increased total dissolved solids by 19% in the CMD-affected river. Coal mine drainage decreased absorption coefficient a(350) and absorption spectral slope S_275-295 of DOM in the CMD-affected river; hence, DOM molecular size increased with decreasing S_275-295. Three-dimensional fluorescence excitation-emission matrix spectroscopy and parallel factor analysis identified humic-like C1, tryptophan-like C2, and tyrosine-like C3 in the CMD-affected river and coal mine drainage. DOM in the CMD-affected river mainly originated from microbial and terrestrial sources, with strong endogenous characteristics. The ultra-high-resolution Fourier transform ion cyclotron resonance mass spectrometry analysis revealed that coal mine drainage had a higher relative abundance of CHO (44.79%), with a higher unsaturation degree of DOM. Coal mine drainage decreased the AI_mod,wa, DBE_wa (double bond equivalents), O_wa, N_wa, and S_wa values and increased the relative abundance of the O₃S₁ species with DBE of 3 and carbons number range of 15-17 at the CMD inlet to the river channel. Moreover, coal mine drainage with the higher protein content increased the protein content of water at the CMD inlet to the river channel and the downstream river. DOM compositions and proprieties in coal mine drainage were investigated to further understand the influence of organic matter on heavy metals in future study.

Transformation of dissolved organic matter during UV/peracetic acid treatment

Peracetic acid combined ultraviolet (UV/PAA) process has garnered growing attention as a promising advanced oxidation process (AOP) for wastewater treatment, but the corresponding transformation of ubiquitous dissolved organic matter (DOM) under this AOP remains unknown. This study systematically investigated the changes in characteristics and composition of DOM under UV/PAA, as well as the underlying mechanisms by multiple spectroscopic analyses and Fourier transform ion cyclotron resonance mass spectrometry. UV/PAA treatment dramatically decreased aromaticity, apparent molecular weight, and fluorescent abundance of DOM with the production of more oxidized and saturated compounds. The reactive species (i.e., ^·OH and CH₃C(O)O^·/CH₃C(O)OO^·) in UV/PAA contributed primarily to DOM changes but showed different reaction selectivity and mechanisms. ^·OH reacts with DOM components and mainly yields oxygenation products via a radical addition pathway. Comparatively, the electron transfer route is more likely to occur in CH₃C(O)O^·/CH₃C(O)OO^·-induced DOM transformation. Aside from oxygenation products, electron transfer could exclusively generate decarboxylation products and distinguishes CH₃C(O)O^·/CH₃C(O)OO^·-based AOPs from ^·OH-based AOPs. These findings significantly improve knowledge of DOM alterations under UV/PAA AOP at both the bulk and molecular levels.

Variations in dissolved organic matter chemistry on a vertical scale in the eastern Indian Ocean

Oceans cover approximately 71% of the Earth's surface area, which is why some people refer to the Earth as a large water sphere. Marine dissolved organic matter (DOM) constitutes the main carbon pool for biogeochemical cycles and plays an important role in global carbon dynamics. Here, the molecular composition and component characteristics of surface (5 m), deep chlorophyll maximum (DCM), and deep (2000 m) layer DOM in the eastern Indian Ocean (EIO) were investigated using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and three-dimensional fluorescence spectroscopy. Thousands of individual DOM formulas (approximately 3716-6986 formulas) were detected at 100-700 Da, showing a Gaussian distribution. The elements carbon (C), hydrogen (H), oxygen (O), nitrogen (N) and sulfur (S) were detected and constituted four formula classes in solid-phase extracted marine DOM samples. Furthermore, the order of the percent intensity of the formulas was CHO > CHNO > CHOS > CHNOS. Carboxylic-rich alicyclic molecule (CRAM) compounds, as part of recalcitrant DOM (RDOM), were detected at 61.32%-78.77% (by intensity). In addition, the concept of islands of stability (IOS, approximately 3.99%-11.22%) has been proposed in this study, representing the most stable components in the marine environment. Such molecular formulas as described above probably contribute to increased RDOM content in the EIO and potentially reflect enhanced accumulation or sequestration of RDOM in the deep layer. The variation in the spectroscopic indices (FI, β/α, BIX, and HIX) and fluorescent components (C1 to C4) with depth indicates a shift from protein-like to humic-like components, leading to gradual aging of the water column. In brief, this study relies on data from marine DOM in the EIO to provide a molecular and chemical background for global models of marine DOM production, transformation and sequestration.

Machine-learning assisted molecular formula assignment to high-resolution mass spectrometry data of dissolved organic matter

High-resolution mass spectrometry (HRMS) provides molecular compositional information of dissolved organic matter (DOM) through isotopic assignment from the molecular mass. However, due to the inevitable deviation of molecular mass measurement and the limitation of resolving power, multiple possible solutions frequently occur for a given molecular mass. Lowering the mass deviation threshold and adding assignment restriction rules are often applied to exclude the incorrect solutions, which generally involves time-consuming manual post-processing of mass data. To improve the result accuracy in an automated manner, we developed a molecular formula assignment algorithm based on machine-learning technology. The method integrated a logistic regression model using manually corrected isotopic composition and the peak features of HRMS data (m/z, signal-to-noise ratio, isotope type, and number, etc.) as training data. The developed model can evaluate the correctness of a candidate formula for the given mass peak based on the peak features. The method was verified by various DOM samples FT-ICR MS data (direct infusion negative mode electrospray), achieving a ∼90% accuracy (compared to the traditional approach) for formula assignment. The method was applied to a series of NOM samples and showed a significant improvement in formula assignment compared with the mass matching method.

Probing Molecular-Level Dynamic Interactions of Dissolved Organic Matter with Iron Oxyhydroxide via a Coupled Microfluidic Reactor and an Online High-Resolution Mass Spectrometry System

The interactions between dissolved organic matter (DOM) and iron (Fe) oxyhydroxide are crucial in regulating the biogeochemical cycling of nutrients and elements, including the preservation of carbon in soils. The mechanisms of DOM molecular assembly on mineral surfaces have been extensively studied at the mesoscale with equilibrium experiments, yet the molecular-level evolution of the DOM-mineral interface under dynamic interaction conditions is not fully understood. Here, we designed a microfluidic reactor coupled with an online solid phase extraction (SPE)-LC-QTOF MS system to continually monitor the changes in DOM composition during flowing contact with Fe oxyhydroxide at circumneutral pH, which simulates soil minerals interacting with constant DOM input. Time-series UV-visible absorption spectra and mass spectrometry data showed that after aromatic DOM moieties were first preferentially sequestered by the pristine Fe oxyhydroxide surface, the adsorption of nonaromatic DOM molecules with greater hydrophobicity, lower acidity, and lower molecular weights (<400) from new DOM solutions was favored. This is accompanied by a transition from mineral surface chemistry-dominated adsorption to organic-organic interaction-dominated adsorption. These findings provide direct molecular-level evidence to the zonal model of DOM assembly on mineral surfaces by taking the dynamics of interfacial interactions into consideration. This study also shows that coupled microfluidics and online high-resolution mass spectrometry (HRMS) system is a promising experimental platform for probing microscale environmental carbon dynamics by integrating in situ reactions, sample pretreatment, and automatic analysis.

Response of dissolved organic matter chemistry to flood control of a large river reservoir during an extreme storm event

With the frequent occurrence of extreme floods under global climate change-induced storm events, reservoir operation has been highlighted for river flood control, complicating the transport and transformation of riverine dissolved organic matter (DOM), one of the largest reactive carbon pools on earth. In particular, the response of riverine DOM chemistry to reservoir flood control during extreme storm events is still unclear. To fill this knowledge gap, the mechanism of DOM variation in Yangtze River with the world's largest Three Gorges Reservoir (TGR) operation during an extreme storm event was explored. Optical and molecular properties of DOM varied significantly from upstream to downstream in non-TGR area, while no significant variation in DOM chemistry was observed in TGR area. The results uncovered a short time transformation of DOM from non-TGR area to TGR area, demonstrating that although storm event induced chemodiversity bloom of riverine DOM, flood control of TGR "re-constrained" DOM to more similar chemistry mainly under the influence of turbidity involved DOM transformation (e.g., adsorption/desorption and flocculation). Furthermore, combined with the hydrological information, we found that although TGR temporarily blocked dissolved organic carbon (DOC) flow during the flood event, the abundance of biologically recalcitrant DOC increased in TGR, which would contribute to its further transportation to downstream watershed. This study emphasizes the impact of TGR on extreme storm event-induced DOM dynamics, which also hints a better understanding of the crucial role of anthropogenic activity in affecting carbon cycling under extreme climate change.

Development of a Gaussian-Based Alignment Algorithm for the Ultrahigh-Resolution Mass Spectra of Dissolved Organic Matter

The alignment of ultrahigh-resolution mass spectra (UHR-MS) is critical to inspect the presence of unique and common peaks across multiple UHR-MS spectra. However, few attempts have been conducted to develop an automated alignment method. In this study, a novel automated alignment algorithm, namely, FTMSCombine, that follows a Gaussian distribution of mass errors was developed and then integrated with existing FTMSCalibrate and TRFu algorithms to establish an open-source analysis platform, namely, FTMSAnalysis, for the UHR-MS analysis of the dissolved organic matter. The developed FTMSCombine was capable of automatically aligning peaks across different UHR-MS spectra by averaging the m/z values of each peak cluster, although the alignment should be restricted to Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) spectra collected by instruments under similar conditions. The FTMSCombine exhibited an insignificant difference in the reproducibility of chemical formulae but significantly higher mass accuracy than the ICBM-OCEAN. In addition to improving the overall mass accuracy of the whole UHR-MS dataset, the FTMSCombine could effectively exclude scatters or noise peaks using an optional rule that restricts peaks (continuously) detected in at least a certain number of spectra in the UHR-MS spectra dataset. The successfully established FTMSAnalysis (freely available in the Supporting Information of this study) is of great potential in automatically analyzing UHR-MS spectra for dissolved organic matter (DOM) and will largely facilitate the elucidation of DOM chemodivesity by UHR-MS techniques including FTICR-MS.

Molecular-level transformation of refractory organic matter during flocculation-ultraviolet/peroxymonosulfate treatment of MBR-treated landfill leachate

Refractory organic matter in membrane bioreactor effluent resulting from landfill leachate treatment has a complex composition. This paper identified the transformation mechanism of organic matter in a flocculation-ultraviolet (UV)/peroxymonosulfate (PMS) system at the molecular level using electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry. The results showed that the flocculation system was able to remove a large amount of dissolved organic matter (DOM) with high oxidation and unsaturation/saturation. UV radiation displayed a relatively strong reactivity for DOM with an electron-rich structure, which it can transform into DOM with lower aromaticity through photolysis and photosensitivity, although the effectiveness of the transformation was poor. In comparison, due to the action of reactive oxygen species, the UV/PMS system can enable reactions such as demethylation, dehydrogenation, decarboxylation, dehydroxylation, ring cleavage, and decarbonylation. It can remove approximately 60% quantity of the total DOM and produce DOM featuring a higher degree of oxidation and saturation than that of the UV system alone. The results showed that the UV/PMS system was a complementary of flocculation in DOM removal from the membrane bioreactor effluent, while the system also resulted in a large number of sulfuric compounds; thus, requiring further evaluation of its ecological effects.

Effects of dissolved organic matter molecules on the sequestration and stability of uranium during the transformation of Fe (oxyhydr)oxides

Amorphous ferrihydrite (Fh) is abundant in aquatic environments and sediments, and often coprecipitates with dissolved organic matter (DOM) to form mineral-organic aggregates. The Fe(II)-catalyzed transformation of Fh to crystalline Fe (oxyhydr)oxides (e.g., goethite) can result in the changes of uranium (U) species, but the effects of DOM molecules on the sequestration and stability of U during Fe (oxyhydr)oxides transformation are poorly understood. In this study, the associations of DOM molecules with U during the coprecipitation of DOM with Fh were evaluated, and the effects of DOM molecules on the kinetics of U release during Fe (oxyhydr)oxides transformation were investigated using a combination of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), X-ray photoelectron spectroscopy (XPS), and kinetic experiments. FT-ICR-MS results indicated that, in addition to phenolic and polyphenolic compounds with higher O/C ratios, portions of phenolic compounds with lower O/C ratios and aliphatic compounds were also contributed to UO₂²⁺ binding when Fh coprecipitated with DOM. In comparison, phenolic and polyphenolic compounds with higher O/C ratios and condensed aromatics were preferentially retained on Fe (oxyhydr)oxides during the transformation. XPS results further suggested that the coprecipitated DOM molecules facilitated the reduction of U(VI) to U(IV) during the transformation, possibly through providing electrons or acting as electron shuttles. The kinetic experiment results indicated that the transformation processes accelerated U release from Fe (oxyhydr)oxides, but the coprecipitated DOM molecules slowed down U release. Our results contribute to understanding the behaviors of U and predicting the sequestration of U in the environment.

Transformation of dissolved organic matter in landfill leachate during a membrane bioreactor treatment

In this study, a cutting-edge mass spectrometry (MS) technique, Orbitrap fusion MS with ultrahigh resolution, was used to analyze the molecular composition, chemical properties, formation mechanism, and environmental impact of refractory dissolved organic matter (rDOM) in leachate. The results showed that the bioavailable DOM (bDOM) and rDOM constituents varied substantially during the biological treatment of landfill leachate. Compared with bDOM, the rDOM in leachate had a higher degree of unsaturation, aromaticity, and oxidation, and a larger molecular weight, and contained more organic matter with benzene ring and biphenyl structures. Using high-throughput 16S rRNA sequencing, metagenomics, the Kendrick mass defect (KMD), and a mass difference network (MDiN), it was found that rDOM in leachate is generated through carboxylation (+COO), dehydro-oligomerization (-H₂), and chain scission (-CH₂) pathways due to the activity of microbes such as Patescibacteria, Chloroflexi, and Proteobacteria. Compared with Suwannee River fulvic acid (SRFA), the rDOM in leachate contained more organics with nitrogen, sulfur, benzene rings, and biphenyls. If the rDOM in leachate enters the environment it will affect the composition of the original organic matter, and its biogeochemical transformation and environmental fate will then need to be monitored and may require special attention.

Green Tides Significantly Alter the Molecular Composition and Properties of Coastal DOC and Perform Dissolved Carbon Sequestration

Despite green tides (or macroalgal blooms) having multiple negative effects, it is thought that they have a positive effect on carbon sequestration, although this aspect is rarely studied. Here, during the world's largest green tide (caused by Ulva prolifera) in the Yellow Sea, the concentration of dissolved organic carbon (DOC) increased by 20-37% in intensive macroalgal areas, and thousands of new molecular formulas rich in CHNO and CHOS were introduced. The DOC molecular species derived from U. prolifera constituted ∼18% of the total DOC molecular species in the seawater of bloom area, indicating the profound effect that green tides have on shaping coastal DOC. In addition, 46% of the macroalgae-derived DOC was labile DOC (LDOC), which had only a short residence time due to rapid microbial utilization. The remaining 54% was recalcitrant DOC (RDOC) rich in humic-like substances, polycyclic aromatics, and highly aromatic compounds that resisted microbial degradation and therefore have the potential to play a role in long-term carbon sequestration. Notably, source analysis showed that in addition to the microbial carbon pump, macroalgae are also an important source of RDOC. The number of RDOC molecular species contributed by macroalgae even exceed (77 vs 23%) that contributed by microorganisms.

You Exude What You Eat: How Carbon-, Nitrogen-, and Sulfur-Rich Organic Substrates Shape Microbial Community Composition and the Dissolved Organic Matter Pool

Phytoplankton is the major source of labile organic matter in the sunlit ocean, and they are therefore key players in most biogeochemical cycles. However, studies examining the heterotrophic bacterial cycling of specific phytoplankton-derived nitrogen (N)- and sulfur (S)-containing organic compounds are currently lacking at the molecular level. Therefore, the present study investigated how the addition of N-containing (glycine betaine [GBT]) and S-containing (dimethylsulfoniopropionate [DMSP]) organic compounds, as well as glucose, influenced the microbial production of new organic molecules and the microbial community composition. The chemical composition of microbial-produced dissolved organic matter (DOM) was analyzed by ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) demonstrating that CHO-, CHON-, and CHOS-containing molecules were enriched in the glucose, GBT, and DMSP experiments, respectively. High-throughput sequencing showed that Alteromonadales was the dominant group in the glucose, while Rhodobacterales was the most abundant group in both the GBT and DMSP experiments. Cooccurrence network analysis furthermore indicated more complex linkages between the microbial community and organic molecules in the GBT compared with the other two experiments. Our results shed light on how different microbial communities respond to distinct organic compounds and mediate the cycling of ecologically relevant compounds. IMPORTANCE Nitrogen (N)- and sulfur (S)-containing compounds are normally considered part of the labile organic matter pool that fuels heterotrophic bacterial activity in the ocean. Both glycine betaine (GBT) and dimethylsulfoniopropionate (DMSP) are representative N- and S-containing organic compounds, respectively, that are important phytoplankton cellular compounds. The present study therefore examined how the microbial community and the organic matter they produce are influenced by the addition of carbohydrate-containing (glucose), N-containing (GBT), and S-containing (DMSP) organic compounds. The results demonstrate that when these carbon-, N-, and S-rich compounds are added separately, the organic molecules produced by the bacteria growing on them are enriched in the same elements. Similarly, the microbial community composition was also distinct when different compounds were added as the substrate. Overall, this study demonstrates how the microbial communities metabolize and transform different substrates thereby, expanding our understanding of the complexity of links between microbes and substrates in the ocean.

Experimental Insight into the Enigmatic Persistence of Marine Refractory Dissolved Organic Matter

More than 90% of marine dissolved organic matter (DOM) is biologically recalcitrant. This recalcitrance has been attributed to intrinsically refractory molecules or to low concentrations of molecules, but their relative contributions are a long-standing debate. Characterizing the molecular composition of marine DOM and its bioavailability is critical for understanding this uncertainty. Here, using different sorbents, DOM was solid-phase extracted from coastal, epipelagic, and deep-sea water samples for molecular characterization and was subjected to a 180-day incubation. ¹H nuclear magnetic resonance spectroscopy and ultra-high-resolution mass spectrometry (UHRMS) analyses revealed that all of the DOM extracts contained refractory carboxyl-rich alicyclic molecules, accompanied with minor bio-labile components, for example, carbohydrates. Furthermore, dissolved organic carbon concentration analysis showed that a considerable fraction of the extracted DOM (86-95%) amended in the three seawater samples resisted microbial decomposition throughout the 180-day heterotrophic incubation, even when concentrated threefold. UHRMS analysis revealed that DOM composition remained mostly invariant in the 180-day deep-sea incubations. These results underlined that the dilution and intrinsic recalcitrance hypotheses are not mutually exclusive in explaining the recalcitrance of oceanic DOM, and that the intrinsically refractory DOM likely has a relatively high contribution to the solid-phase extractable DOM in the ocean.